MAPLE (MAximum Parsimonius Likelihood Estimation) is a maximum likelihood phylogenetic software tailored to large genomic datasets of closely related sequences, such as SARS-CoV-2 genomes. It aims at improving the speed and accuracy of phylogenetic estimation in genomic epidemiology by adopting ad hoc algorithms and approximations. MAPLE allows online phylogenetic inference, sample placement, lineage assignment, and has now a range of evolutionary models implemented, including mutation rate variation and recurrent sequence errors.

For more details see our publication 

https://www.nature.com/articles/s41588-023-01368-0 

and our software page 

https://github.com/NicolaDM/MAPLE.